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Re: Pneumaticity in Triassic pterosaurs

----- Original Message ----- From: "David Peters" <davidpeters@att.net>
Sent: Sunday, May 17, 2009 3:36 PM
Subject: Re: Pneumaticity in Triassic pterosaurs

First of all, if Dr. Laurin was a referee, then you just blew his anonymity. I hope that's okay with your mentor.

He almost always signs his reviews... are you sure he didn't this time? Also, I don't know for which journal he reviewed your manuscript; didn't you send it to several?

Second, specifically, how, in your view, does a phylogenetic data matrix differ from a phenetic one when dealing with fossil organisms? Are not both concerned with morphology, characters and ratios?

We have _been_ through this! Right after Steve Brusatte and colleagues published their science paper on the speed of morphological evolution of various archosaur clades in the Triassic, you noticed that the dataset in the supp. inf. didn't give the tree that also was in the supp. inf., and Steve came in and explained why! Here! Onlist! And before he did, several other people discussed with you about this!

<headshake> Brain like a noodle sieve.

Short answer: It is very easy to put characters into a matrix that are correlated with each other, or that lack phylogenetic signal because they evolve too fast for the problem in question (imagine feather color in an analysis of Neornithes -- this is a very real problem in molecular phylogenetics, where it's called "saturation"); in a phenetic analysis, this doesn't matter (or may even be desired, as it was in that of Brusatte et al., who optimized their carefully designed phenetic matrix onto a phylogenetic tree to see which changes had happened along each internode), but it can seriously screw up a phylogenetic analysis. If two correlated characters are in the same matrix, that's like having a single character with double weight in it, and there's no reason for that double weight. It's arbitrary, and will give a wrong result. If a character without phylogenetic signal is in the matrix, that means there's random noise in the matrix which will destabilize the tree and may support a slightly less parsimonious one than the one that would be found without it.

And phylogenetic analyses are often very sensitive to "garbage in, garbage out". Fig. 10 of the paper by Anne Warren in the December 2007 issue of JVP (on the Early Carboniferous tetrapod *Ossinodus*) shows two totally different trees that were derived from fairly large matrices that differed in a single cell. Check it out and be amazed. And here http://dpc.uba.uva.nl/ctz/vol77/nr03/art02 is a whole paper on that phenomenon.

Long answer: Look it up. Steve's explanation was excellent as far as I remember.

Third, if a given matrix and its scores deliver a single MPT in which all sister taxa are similar in size, shape, niche and chronology, isn't that a good result?

A result can't be better than the matrix it's calculated from... :-)

> I can show you the path of most parsimony if
you're interested.

Erm, PAUP* will do that... :-)

By that I meant, if you are accidentally excluding any pertinent taxa, you should be told.

Oh, sure. I'll send you the taxon list once I'm done with making it. But I don't think you'll find any omissions; I'm totally megalomaniac on taxon inclusion. :-)

And then on to the M. Habib replies:

(More precisely, my reply to his reply.)

Probably the idea is that if taxa are too distant
phenetically -- that is, by a subjective, intuitive estimate
of phenetic distance, not even by any attempt at
quantification --, they can't be sister-groups.

No, simply that a larger test found better sister taxa here excluded.

I was talking about your use of "family resemblance".

- For the probably twentieth time, the vertebrate fossil
record -- let alone our knowledge of it!!! -- simply
isn't complete enough that we could expect to do what
the Unnameable Ones ask us to do (to present them a complete
series of transitional fossils documenting each and every
speciation-or-whatever between two arbitrary endpoints).

Respectfully, that's an opinion, David.

Show me. :-)

Let me advance an argument: As of today, there are 6,487 known extant species of lissamphibians (http://www.amphibiaweb.org/, bottom). Let's ignore all those whose ecological niches didn't exist in the Early Permian. I suppose this means a few thousand species of rainforest frogs. We might be left with... let's err on the side of caution and say only 1,000 species.

Then let's find out how many potential ecological analogs to those lissamphibians we know from the Early Permian fossil record. Maybe 20 species of "branchiosaurs"; maybe 20 species, probably less, of (other?) amphibamids; a handful species of "microsaurs", not all of which count because some are more analogous to amphisbaenians or maybe other squamates; seymouriamorphs count because of their aquatic larvae, but for the entire Early Permian (Cisuralian) this adds at most, like, 10 species (half of those in places with very uncertain stratigraphy)...

I estimate about 50, distributed through thirty million years. Today, right now, we seem to have two hundred times that. If that isn't a red flag that shows us how incomplete the fossil record is...

Also, when you say 'complete series' I hope you don't mean every mother's son. What I'm saying is you'll be able to line them up like the famous Australopithecus to Homo sapiens march.

Famous march?

You seem to have missed the last few decades on that one. It's a pretty bewildering bush. We don't even know where *Kenyanthropus* and *Homo* fit into the *Australopithecus* tree, or maybe outside of it...

Or as I did from bacteria to humans in "From the Beginning" (1991)now available only from Amazon.

The two reviews I find on Amazon are not detailed enough to explain what you mean...

Incidentally, the "from bacteria" part just got more interesting:

James A. Lake, Jacqueline A. Servin, Craig W. Herbold & Ryan G. Skophammer: Evidence for a new root of the tree of life, Systematic Biology 57(6), 835 -- 843 (December 2008)


Directed indels, insertions or deletions wihtin paralogous genes, have the potential to root the tree of life. There we apply the top-down rooting algorithm to indels found in PyrD (dihydroorotate dehydrogenase), a key enzyme involved in the de novo biosynthesis of pyrimidines, and HisA (P-ribosylformimino-AICAR-P-isomerase), an essential enzyme in the histidine biosynthesis pathway [these two are paralogous to each other, having arisen from a gene duplication before the origin of the crown-group of life]. Through the comparison of each indel with its two paralogous outgroups [the second being a gene called HisF], we exclude the root of the tree of life from the clade that encompasses the Actinobacteria, the double-membrane prokaryotes [gram-negative bacteria], and their last common ancestor. In combination with previous indel rooting studies excluding the root from a clade consisting of the Firmicutes [gram-positive bacteria], the Archaea, and their last common ancestor, this provides evidence for a unique eubacterial root for the tree of life located between the actinobacterial--double-membrane clade and the archaeal-firmicute clade. Mapping the distributions of genes involved in peptidoglycan and lipid synthesis onto this rooted tree parsimoniously implies that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer.

Another surprise, published earlier, is that Firmicutes is paraphyletic: the bacilli are more closely related to us than the clostridia. Sum (from fig. 2):

| `--gram-negative bacteria
`--+--Archaea (imaginably paraphyletic)
`--Eukaryota, except for the many genes which come from gram-negative bacteria (probably all from the mitochondrium)

The whole idea is just to get a picture of what really happened.

But that picture comes from reading the tree, not the other way around. Phylogeny first, scenario second.

In fact, that's not limited to vertebrates. It does not
even hold for ammonites and conodonts; that's why
stratophenetics (using total resemblance and stratigraphy to
construct a tree and then interpret that tree as a
phylogenetic one) does not work.

Okay. If you're referring to my submission,

I'm not.

the stratigraphy was added after the phylogenetics, just to see where things fell.

I didn't see that part, and there's nothing wrong with it. There's also stratocladistics, which tries to include stratigraphic information in its parsimony decisions. My point was that _even for taxa with a much better fossil record than vertebrates_ the fossil record is too incomplete to allow stratophenetics to work, in other words, too incomplete that we could expect to be able to see all the family resemblance you are talking about. That you didn't do stratophenetics is not relevant to that point.